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220 results for “functional sequencing”
Sequence-structure-function relationships in class I MHC: a local frustration perspective
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Shallow shotgun sequencing of the microbiome recapitulates 16S amplicon results and provides functional insights
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Divergence in coding sequence and expression of different functional categories of immune genes between two wild rodent species
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Database for mi-faser: Functional sequencing read annotation for high precision microbiome analysis
<p><strong>[Database for mi-faser]</strong></p> <p><strong>mi-faser: </strong><em>microbiome - functional annotation of sequencing reads</em></p> <p>A super-fast ( < 20min/10GB of reads ) and accurate ( > 90% precision ) method for annotation of molecular functionality encoded in sequencing read data without the need for assembly or gene finding.</p> <p>Web Service: http://services.bromberglab.org/mifaser/|<br> Repository: https://bitbucket.org/bromberglab/mifaser_base/</p>
Data from: Biodiversity assessment using next-generation sequencing: comparison of phylogenetic and functional diversity between Nebraska grasslands
Global biodiversity is declining rapidly as a consequence of anthropogenic changes to the environment. Traditional diversity indices such as species richness have been used to assess biodiversity, but recent arguments call for a more comprehensive assessment that includes both phylogenetic and functional diversity (PD and FD, respectively). Many PD metrics have been developed, but few empirical studies have compared metrics across sites with the goal of understanding their application to characterizing biodiversity. In this study, 17 PD metrics, four traditional diversity indices, and one measure of FD were calculated and compared between two Nebraska grasslands. PD metrics were calculated from robust phylogenies estimated from next-generation sequencing data of 45 species. Traditional indices were calculated using species abundance data, and FD was quantified by measuring the phylogenetic signal, K, of specific leaf area (SLA). Results showed that PD metrics and traditional indices were not always correlated, and various PD metrics characterized biodiversity differently. In addition, phylogenies estimated from >80 genes were more robust than single- or dual-gene phylogenies resulting in more reliable PD metrics. K of SLA indicated random trait assembly in all sites. Results suggested that metrics that identify phylogenetic structure and relatedness can provide information to conservation planners about the ability of a community to persist in an unpredictable future. A combination of these results with those of future investigations applying PD and FD metrics to varying communities will support concrete recommendations to conservation planners about how to incorporate these metrics into the selection of priority regions.
Data from: Predicting function from sequence in a large multifunctional toxin family
Venoms contain active substances with highly specific physiological effects and are increasingly being used as sources of novel diagnostic, research and treatment tools for human disease. Experimental characterisation of individual toxin activities is a severe rate-limiting step in the discovery process, and in-silico tools which allow function to be predicted from sequence information are essential. Toxins are typically members of large multifunctional families of structurally similar proteins that can have different biological activities, and minor sequence divergence can have significant consequences. Thus, existing predictive tools tend to have low accuracy. We investigated a classification model based on physico-chemical attributes that can easily be calculated from amino-acid sequences, using over 250 (mostly novel) viperid phospholipase A2 toxins. We also clustered proteins by sequence profiles, and carried out in-vitro tests for four major activities on a selection of isolated novel toxins, or crude venoms known to contain them. The majority of detected activities were consistent with predictions, in contrast to poor performance of a number of tested existing predictive methods. Our results provide a framework for comparison of active sites among different functional sub-groups of toxins that will allow a more targeted approach for identification of potential drug leads in the future.
Sequence and functional analyses of native plasmids from plant pathogenic Gammaproteobacteria: comparative genomics, conjugative mobilization and fitness effects
<p>These data tables are part of the Supplementary Material for Chapter I of the thesis titled <em>"Sequence and Functional Analyses of Native Plasmids from Plant-Pathogenic Gammaproteobacteria: Comparative Genomics, Conjugative Mobilization, and Fitness Effects."</em></p>
Data from: A functional diversity approach of crop sequences reveals that weed diversity and abundance show different responses to environmental variability
1. Combining several crop species and associated agricultural practices in a crop sequence has the potential to control weed abundance while promoting weed diversity in arable fields. However, how the variability of environmental conditions that arise from crop sequences affects weed diversity and abundance remains poorly understood, with most studies to-date simply opposing weed communities in monoculture and in crop rotation. Here, we describe crop sequences along gradients of disturbance and resource variability using a crop functional trait and associated agricultural practices. We tested the hypothesis that variability of disturbances reduces weed abundance while variability of resources promotes weed diversity. 2. We used functional Hill's numbers to compute crop sequence functional diversity based on sowing date, herbicide spectrum and crop height - these are the respective proxies of disturbance timings, disturbance types and light availability. Using a large-scale weed monitoring database, we assessed crop sequence diversity for 1045 crop sequences of five consecutive cropping seasons. We computed weed richness and abundance at pluri-annual (pool of weeds observed across five cropping seasons) and annual (pool of weeds observed during a winter cereal cropping season preceded by five cropping seasons) scales. We also accounted for herbicide and tillage intensities to test whether management intensity affects the response of weed diversity and abundance to crop sequence diversity. 3. At the pluri-annual scale, weed richness increased with the diversity of crop height and sowing date while weed abundance decreased with sowing date diversity. Annual weed richness decreased with sowing date diversity while annual weed abundance poorly relied on crop sequence diversity. 4. Synthesis and applications. This study establishes a scientific basis for designing crop sequences according to specific weed management goals. We show that farmers may enhance arable weed diversity on a pluri-annual scale by sequentially sowing crop species that differ in their competitive ability and sowing date. They may also achieve a better control of weed abundance by increasing the diversity of crop sowing dates across the crop sequence.
Data from: Biodiversity assessment using next-generation sequencing: comparison of phylogenetic and functional diversity between Nebraska grasslands
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Data from: Predicting function from sequence in a large multifunctional toxin family
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Data from: A functional diversity approach of crop sequences reveals that weed diversity and abundance show different responses to environmental variability
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Data from: Use of genotyping-by-sequencing data to develop a high-throughput and multi-functional SNP panel for conservation applications in Pacific lamprey
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Data from: Elucidating the functional evolution of heat sensors among Xenopus species adapted to different thermal niches by ancestral sequence reconstruction
Ambient temperature fluctuations are detected via the thermosensory system which allows animals to seek preferable thermal conditions or escape from harmful temperatures. Evolutionary changes in thermal perception have thus potentially played crucial roles in niche selection. The genus Xenopus (clawed frog) is suitable for investigating the relationship between thermal perception and niche selection due to their diverse latitudinal and altitudinal distributions. Here we performed comparative analyses of the neuronal heat sensors TRPV1 and TRPA1 among closely related Xenopus species (X. borealis, X. muelleri, X. laevis, and X. tropicalis) to elucidate their functional evolution and to assess whether their functional differences correlate with thermal niche selection among the species. Comparison of TRPV1 among four extant Xenopus species and reconstruction of the ancestral TRPV1 revealed that TRPV1 responses to repeated heat stimulation were specifically altered in the lineage leading to X. tropicalis which inhabits warmer niches. Moreover, the thermal sensitivity of TRPA1 was lower in X. tropicalis than the other species, although the thermal sensitivity of TRPV1 and TRPA1 was not always lower in species that inhabit warmer niches than the species inhabit cooler niches. However, a clear correlation was found in species differences in TRPA1 activity. Heat-evoked activity of TRPA1 in X. borealis and X. laevis, which are adapted to cooler niches, was significantly higher than in X. tropicalis and X. muelleri which are adapted to warmer niches. These findings suggest that the functional properties of heat sensors changed during Xenopus evolution, potentially altering the preferred temperature ranges among species.
Data from: The phylogenetic utility and functional constraint of microRNA flanking sequences
MicroRNAs (miRNAs) have recently risen to prominence as novel factors responsible for post-transcriptional regulation of gene expression. miRNA genes have been posited as highly conserved in the clades in which they exist. Consequently, miRNAs have been used as rare genome change characters to estimate phylogeny by tracking their gain and loss. However, their short length (21–23 bp) has limited their perceived utility in sequenced-based phylogenetic inference. Here, using reference taxa with established phylogenetic relationships, we demonstrate that miRNA sequences are of high utility in quantitative, rather than in qualitative, phylogenetic analysis. The clear orthology among miRNA genes from different species makes it straightforward to identify and align these sequences from even fragmentary datasets. We also identify significant sequence conservation in the regions directly flanking miRNA genes, and show that this too is of utility in phylogenetic analysis, as well as highlighting conserved regions that will be of interest to other fields. Employing miRNA sequences from 12 sequenced drosophilid genomes, together with a Tribolium castaneum outgroup, we demonstrate that this approach is robust using Bayesian and maximum-likelihood methods. The utility of these characters is further demonstrated in the rhabditid nematodes and primates. As next-generation sequencing makes it more cost-effective to sequence genomes and small RNA libraries, this methodology provides an alternative data source for phylogenetic analysis. The approach allows rapid resolution of relationships between both closely related and rapidly evolving species, and provides an additional tool for investigation of relationships within the tree of life.
Data from: Phylogenetic Relationships of Fig Wasps Pollinating Functionally Dioecious Ficus Based on Mitochondrial DNA Sequences and Morphology
The obligate mutualism between pollinating fig wasps in the family Agaonidae (Hymenoptera: Chalcidoidea) and Ficus species (Moraceae) is often regarded as an example of coevolution but little is known about the history of the interaction and understanding the origin of functionally dioecious fig pollination has been especially difficult. The phylogenetic relationships of fig wasps pollinating functionally dioecious Ficus were inferred from mitochondrial cytochrome oxidase gene sequences (mtDNA) and morphology. Separate and combined analyses indicated that the pollinators of functionally dioecious figs are not monophyletic. However, pollinator relationships were generally congruent with host phylogeny and support a revised classification of Ficus. Ancestral changes in pollinator ovipositor length were also correlated with changes in fig breeding system. In particular, the relative elongation of the ovipositor was associated with the repeated loss of functionally dioecious pollination. The concerted evolution of interacting morphologies may bias estimates of phylogeny based on female head characters but homoplasy is not so concerted in other morphological traits. The lesser phylogenetic utility of morphology compared to mtDNA is not due to rampant convergence in morphology but rather to the greater number of potentially informative characters in DNA sequence data and patterns of nucleotide substitution also limit the utility of mtDNA. None the less, inferring the ancestral associations of fig pollinators from the best-supported phylogeny provided strong evidence of host conservatism in this highly specialized mutualism.
Sequence data and structural data utilized in the study and analysis of grain protein function prediction.
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Sequences of Aerobic and Resistance Exercise and Cardio-metabolic Functions in T2D
ClinicalTrials.gov study NCT06145542. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: The phylogenetic utility and functional constraint of microRNA flanking sequences
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Data from: Phylogenetic Relationships of Fig Wasps Pollinating Functionally Dioecious Ficus Based on Mitochondrial DNA Sequences and Morphology
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Data from: Elucidating the functional evolution of heat sensors among Xenopus species adapted to different thermal niches by ancestral sequence reconstruction
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.